loops Namespace Reference

Namespaces
	ccd

Functions
BooleanOptionKey const	loops ("loops")
StringOptionKey const	cen_weights ("loops:cen_weights")
StringOptionKey const	cen_patch ("loops:cen_patch")
FileOptionKey const	input_pdb ("loops:input_pdb")
StringVectorOptionKey const	loop_file ("loops:loop_file")
FileOptionKey const	extended_loop_file ("loops:extended_loop_file")
FileOptionKey const	mm_loop_file ("loops:mm_loop_file")
BooleanOptionKey const	fix_natsc ("loops:fix_natsc")
BooleanOptionKey const	refine_only ("loops:refine_only")
BooleanOptionKey const	fast ("loops:fast")
FileOptionKey const	vall_file ("loops:vall_file")
IntegerVectorOptionKey const	frag_sizes ("loops:frag_sizes")
FileVectorOptionKey const	frag_files ("loops:frag_files")
FileOptionKey const	output_pdb ("loops:output_pdb")
BooleanOptionKey const	debug ("loops:debug")
BooleanOptionKey const	build_initial ("loops:build_initial")
BooleanOptionKey const	extended ("loops:extended")
BooleanOptionKey const	remove_extended_loops ("loops:remove_extended_loops")
BooleanOptionKey const	idealize_after_loop_close ("loops:idealize_after_loop_close")
BooleanOptionKey const	idealize_before_loop_close ("loops:idealize_before_loop_close")
IntegerOptionKey const	select_best_loop_from ("loops:select_best_loop_from")
IntegerOptionKey const	build_attempts ("loops:build_attempts")
IntegerOptionKey const	grow_attempts ("loops:grow_attempts")
RealOptionKey const	random_grow_loops_by ("loops:random_grow_loops_by")
BooleanOptionKey const	accept_aborted_loops ("loops:accept_aborted_loops")
BooleanOptionKey const	strict_loops ("loops:strict_loops")
BooleanOptionKey const	superimpose_native ("loops:superimpose_native")
IntegerVectorOptionKey const	build_specific_loops ("loops:build_specific_loops")
BooleanOptionKey const	random_order ("loops:random_order")
BooleanOptionKey const	build_all_loops ("loops:build_all_loops")
BooleanOptionKey const	fa_closure_protocol ("loops:fa_closure_protocol")
RealOptionKey const	combine_rate ("loops:combine_rate")
BooleanOptionKey const	skip_initial_loop_build ("loops:skip_initial_loop_build")
StringOptionKey const	remodel ("loops:remodel")
StringOptionKey const	intermedrelax ("loops:intermedrelax")
StringOptionKey const	refine ("loops:refine")
StringOptionKey const	relax ("loops:relax")
BooleanOptionKey const	final_clean_fastrelax ("loops:final_clean_fastrelax")
BooleanOptionKey const	relax_with_foldtree ("loops:relax_with_foldtree")
RealOptionKey const	constrain_rigid_segments ("loops:constrain_rigid_segments")
StringOptionKey const	loopscores ("loops:loopscores")
BooleanOptionKey const	timer ("loops:timer")
BooleanOptionKey const	vicinity_sampling ("loops:vicinity_sampling")
RealOptionKey const	vicinity_degree ("loops:vicinity_degree")
RealOptionKey const	neighbor_dist ("loops:neighbor_dist")
IntegerOptionKey const	kic_max_seglen ("loops:kic_max_seglen")
BooleanOptionKey const	kic_recover_last ("loops:kic_recover_last")
BooleanOptionKey const	kic_min_after_repack ("loops:kic_min_after_repack")
BooleanOptionKey const	optimize_only_kic_region_sidechains_after_move ("loops:optimize_only_kic_region_sidechains_after_move")
IntegerOptionKey const	max_kic_build_attempts ("loops:max_kic_build_attempts")
IntegerOptionKey const	remodel_kic_attempts ("loops:remodel_kic_attempts")
IntegerOptionKey const	max_kic_perturber_samples ("loops:max_kic_perturber_samples")
BooleanOptionKey const	nonpivot_torsion_sampling ("loops:nonpivot_torsion_sampling")
BooleanOptionKey const	fix_ca_bond_angles ("loops:fix_ca_bond_angles")
BooleanOptionKey const	kic_use_linear_chainbreak ("loops:kic_use_linear_chainbreak")
BooleanOptionKey const	sample_omega_at_pre_prolines ("loops:sample_omega_at_pre_prolines")
BooleanOptionKey const	allow_omega_move ("loops:allow_omega_move")
BooleanOptionKey const	kic_with_cartmin ("loops:kic_with_cartmin")
BooleanOptionKey const	allow_takeoff_torsion_move ("loops:allow_takeoff_torsion_move")
IntegerOptionKey const	extend_length ("loops:extend_length")
IntegerOptionKey const	perturb_outer_cycles ("loops:perturb_outer_cycles")
IntegerOptionKey const	refine_outer_cycles ("loops:refine_outer_cycles")
IntegerOptionKey const	max_inner_cycles ("loops:max_inner_cycles")
IntegerOptionKey const	repack_period ("loops:repack_period")
RealOptionKey const	remodel_init_temp ("loops:remodel_init_temp")
RealOptionKey const	remodel_final_temp ("loops:remodel_final_temp")
RealOptionKey const	refine_init_temp ("loops:refine_init_temp")
RealOptionKey const	refine_final_temp ("loops:refine_final_temp")
IntegerOptionKey const	gapspan ("loops:gapspan")
IntegerOptionKey const	spread ("loops:spread")
IntegerOptionKey const	kinematic_wrapper_cycles ("loops:kinematic_wrapper_cycles")
IntegerOptionKey const	kic_num_rotamer_trials ("loops:kic_num_rotamer_trials")
BooleanOptionKey const	kic_omega_sampling ("loops:kic_omega_sampling")
RealOptionKey const	kic_bump_overlap_factor ("loops:kic_bump_overlap_factor")
IntegerOptionKey const	minimize_max_iter ("loops:minimize_max_iter")
StringOptionKey const	restrict_kic_sampling_to_torsion_string ("loops:restrict_kic_sampling_to_torsion_string")
BooleanOptionKey const	derive_torsion_string_from_native_pose ("loops:derive_torsion_string_from_native_pose")
BooleanOptionKey const	always_remodel_full_loop ("loops:always_remodel_full_loop")
BooleanOptionKey const	taboo_sampling ("loops:taboo_sampling")
BooleanOptionKey const	taboo_in_fa ("loops:taboo_in_fa")
BooleanOptionKey const	ramp_fa_rep ("loops:ramp_fa_rep")
BooleanOptionKey const	ramp_rama ("loops:ramp_rama")
BooleanOptionKey const	kic_rama2b ("loops:kic_rama2b")
BooleanOptionKey const	kic_leave_centroid_after_initial_closure ("loops:kic_leave_centroid_after_initial_closure")
BooleanOptionKey const	legacy_kic ("loops:legacy_kic")
BooleanOptionKey const	alternative_closure_protocol ("loops:alternative_closure_protocol")
RealOptionKey const	chainbreak_max_accept ("loops:chainbreak_max_accept")
BooleanOptionKey const	debug_loop_closure ("loops:debug_loop_closure")
BooleanOptionKey const	non_ideal_loop_closing ("loops:non_ideal_loop_closing")
RealOptionKey const	scored_frag_cycles ("loops:scored_frag_cycles")
RealOptionKey const	short_frag_cycles ("loops:short_frag_cycles")
RealOptionKey const	rmsd_tol ("loops:rmsd_tol")
RealOptionKey const	chain_break_tol ("loops:chain_break_tol")
BooleanOptionKey const	random_loop ("loops:random_loop")
FileVectorOptionKey const	stealfrags ("loops:stealfrags")
IntegerOptionKey const	stealfrags_times ("loops:stealfrags_times")
RealOptionKey const	coord_cst ("loops:coord_cst")
RealOptionKey const	skip_1mers ("loops:skip_1mers")
RealOptionKey const	skip_3mers ("loops:skip_3mers")
RealOptionKey const	skip_9mers ("loops:skip_9mers")
BooleanOptionKey const	loop_model ("loops:loop_model")
RealOptionKey const	score_filter_cutoff ("loops:score_filter_cutoff")
BooleanOptionKey const	ccd_closure ("loops:ccd_closure")
BooleanOptionKey const	skip_ccd_moves ("loops:skip_ccd_moves")
BooleanOptionKey const	no_randomize_loop ("loops:no_randomize_loop")
BooleanOptionKey const	loops_subset ("loops:loops_subset")
IntegerOptionKey const	num_desired_loops ("loops:num_desired_loops")
RealOptionKey const	loop_combine_rate ("loops:loop_combine_rate")
RealOptionKey const	final_score_filter ("loops:final_score_filter")
BooleanOptionKey const	no_combine_if_fail ("loops:no_combine_if_fail")
BooleanOptionKey const	shorten_long_terminal_loop ("loops:shorten_long_terminal_loop")
IntegerOptionKey const	backrub_trials ("loops:backrub_trials")
RealOptionKey const	looprlx_cycle_ratio ("loops:looprlx_cycle_ratio")
RealOptionKey const	extended_beta ("loops:extended_beta")
BooleanOptionKey const	no_looprebuild ("loops:no_looprebuild")
BooleanOptionKey const	allow_lig_move ("loops:allow_lig_move")
FileOptionKey const	keep_natro ("loops:keep_natro")
IntegerOptionKey const	refine_design_iterations ("loops:refine_design_iterations")

Variables
tuple	p = Pose()
tuple	starting_p = Pose()
tuple	scorefxn_low = create_score_function('cen_std')
tuple	scorefxn_high = create_score_function_ws_patch('standard', 'score12')
int	loop_begin = 77
int	loop_end = 85
int	cutpoint = 81
tuple	my_loop = Loop( loop_begin, loop_end, cutpoint)
tuple	movemap = MoveMap()
tuple	fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")
tuple	mover_3mer = ClassicFragmentMover(fragset3mer,movemap)
tuple	ccd_closure = CCDLoopClosureMover(my_loop, movemap)
tuple	to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid')
tuple	to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard')
tuple	recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p)
tuple	task_pack = TaskFactory.create_packer_task(starting_p)
tuple	pack = protocols.simple_moves.PackRotamersMover( scorefxn_high, task_pack )
tuple	starting_p_centroid = Pose()
tuple	jd = Job_dist("loop_output", 100, scorefxn_high)
int	outer_cycles = 10
int	inner_cycles = 30
float	init_temp = 2.0
float	final_temp = 0.8
tuple	gamma = math.pow((final_temp/init_temp),(1.0/(outer_cycles*inner_cycles)))
	kT = init_temp
tuple	mc = MonteCarlo(p, scorefxn_low, kT)
tuple	my_loops = Loops()
tuple	loop_refine = LoopMover_Refine_CCD(my_loops)
tuple	Lrms = loop_rmsd(p, starting_p, my_loops, True)

Function Documentation

BooleanOptionKey const loops::accept_aborted_loops

(

"loops:accept_aborted_loops"

)

BooleanOptionKey const loops::allow_lig_move

(

"loops:allow_lig_move"

)

BooleanOptionKey const loops::allow_omega_move

(

"loops:allow_omega_move"

)

BooleanOptionKey const loops::allow_takeoff_torsion_move

(

"loops:allow_takeoff_torsion_move"

)

BooleanOptionKey const loops::alternative_closure_protocol

(

"loops:alternative_closure_protocol"

)

BooleanOptionKey const loops::always_remodel_full_loop

(

"loops:always_remodel_full_loop"

)

IntegerOptionKey const loops::backrub_trials

(

"loops:backrub_trials"

)

BooleanOptionKey const loops::build_all_loops

(

"loops:build_all_loops"

)

IntegerOptionKey const loops::build_attempts

(

"loops:build_attempts"

)

BooleanOptionKey const loops::build_initial

(

"loops:build_initial"

)

IntegerVectorOptionKey const loops::build_specific_loops

(

"loops:build_specific_loops"

)

BooleanOptionKey const loops::ccd_closure

(

"loops:ccd_closure"

)

StringOptionKey const loops::cen_patch

(

"loops:cen_patch"

)

StringOptionKey const loops::cen_weights

(

"loops:cen_weights"

)

RealOptionKey const loops::chain_break_tol

(

"loops:chain_break_tol"

)

RealOptionKey const loops::chainbreak_max_accept

(

"loops:chainbreak_max_accept"

)

RealOptionKey const loops::combine_rate

(

"loops:combine_rate"

)

RealOptionKey const loops::constrain_rigid_segments

(

"loops:constrain_rigid_segments"

)

RealOptionKey const loops::coord_cst

(

"loops:coord_cst"

)

BooleanOptionKey const loops::debug

(

"loops:debug"

)

BooleanOptionKey const loops::debug_loop_closure

(

"loops:debug_loop_closure"

)

BooleanOptionKey const loops::derive_torsion_string_from_native_pose

(

"loops:derive_torsion_string_from_native_pose"

)

IntegerOptionKey const loops::extend_length

(

"loops:extend_length"

)

BooleanOptionKey const loops::extended

(

"loops:extended"

)

RealOptionKey const loops::extended_beta

(

"loops:extended_beta"

)

FileOptionKey const loops::extended_loop_file

(

"loops:extended_loop_file"

)

BooleanOptionKey const loops::fa_closure_protocol

(

"loops:fa_closure_protocol"

)

BooleanOptionKey const loops::fast

(

"loops:fast"

)

BooleanOptionKey const loops::final_clean_fastrelax

(

"loops:final_clean_fastrelax"

)

RealOptionKey const loops::final_score_filter

(

"loops:final_score_filter"

)

BooleanOptionKey const loops::fix_ca_bond_angles

(

"loops:fix_ca_bond_angles"

)

BooleanOptionKey const loops::fix_natsc

(

"loops:fix_natsc"

)

FileVectorOptionKey const loops::frag_files

(

"loops:frag_files"

)

IntegerVectorOptionKey const loops::frag_sizes

(

"loops:frag_sizes"

)

IntegerOptionKey const loops::gapspan

(

"loops:gapspan"

)

IntegerOptionKey const loops::grow_attempts

(

"loops:grow_attempts"

)

BooleanOptionKey const loops::idealize_after_loop_close

(

"loops:idealize_after_loop_close"

)

BooleanOptionKey const loops::idealize_before_loop_close

(

"loops:idealize_before_loop_close"

)

FileOptionKey const loops::input_pdb

(

"loops:input_pdb"

)

StringOptionKey const loops::intermedrelax

(

"loops:intermedrelax"

)

FileOptionKey const loops::keep_natro

(

"loops:keep_natro"

)

RealOptionKey const loops::kic_bump_overlap_factor

(

"loops:kic_bump_overlap_factor"

)

BooleanOptionKey const loops::kic_leave_centroid_after_initial_closure

(

"loops:kic_leave_centroid_after_initial_closure"

)

IntegerOptionKey const loops::kic_max_seglen

(

"loops:kic_max_seglen"

)

BooleanOptionKey const loops::kic_min_after_repack

(

"loops:kic_min_after_repack"

)

IntegerOptionKey const loops::kic_num_rotamer_trials

(

"loops:kic_num_rotamer_trials"

)

BooleanOptionKey const loops::kic_omega_sampling

(

"loops:kic_omega_sampling"

)

BooleanOptionKey const loops::kic_rama2b

(

"loops:kic_rama2b"

)

BooleanOptionKey const loops::kic_recover_last

(

"loops:kic_recover_last"

)

BooleanOptionKey const loops::kic_use_linear_chainbreak

(

"loops:kic_use_linear_chainbreak"

)

BooleanOptionKey const loops::kic_with_cartmin

(

"loops:kic_with_cartmin"

)

IntegerOptionKey const loops::kinematic_wrapper_cycles

(

"loops:kinematic_wrapper_cycles"

)

BooleanOptionKey const loops::legacy_kic

(

"loops:legacy_kic"

)

RealOptionKey const loops::loop_combine_rate

(

"loops:loop_combine_rate"

)

StringVectorOptionKey const loops::loop_file

(

"loops:loop_file"

)

BooleanOptionKey const loops::loop_model

(

"loops:loop_model"

)

RealOptionKey const loops::looprlx_cycle_ratio

(

"loops:looprlx_cycle_ratio"

)

BooleanOptionKey const loops::loops

(

"loops"

)

BooleanOptionKey const loops::loops_subset

(

"loops:loops_subset"

)

StringOptionKey const loops::loopscores

(

"loops:loopscores"

)

IntegerOptionKey const loops::max_inner_cycles

(

"loops:max_inner_cycles"

)

IntegerOptionKey const loops::max_kic_build_attempts

(

"loops:max_kic_build_attempts"

)

IntegerOptionKey const loops::max_kic_perturber_samples

(

"loops:max_kic_perturber_samples"

)

IntegerOptionKey const loops::minimize_max_iter

(

"loops:minimize_max_iter"

)

FileOptionKey const loops::mm_loop_file

(

"loops:mm_loop_file"

)

RealOptionKey const loops::neighbor_dist

(

"loops:neighbor_dist"

)

BooleanOptionKey const loops::no_combine_if_fail

(

"loops:no_combine_if_fail"

)

BooleanOptionKey const loops::no_looprebuild

(

"loops:no_looprebuild"

)

BooleanOptionKey const loops::no_randomize_loop

(

"loops:no_randomize_loop"

)

BooleanOptionKey const loops::non_ideal_loop_closing

(

"loops:non_ideal_loop_closing"

)

BooleanOptionKey const loops::nonpivot_torsion_sampling

(

"loops:nonpivot_torsion_sampling"

)

IntegerOptionKey const loops::num_desired_loops

(

"loops:num_desired_loops"

)

BooleanOptionKey const loops::optimize_only_kic_region_sidechains_after_move

(

"loops:optimize_only_kic_region_sidechains_after_move"

)

FileOptionKey const loops::output_pdb

(

"loops:output_pdb"

)

IntegerOptionKey const loops::perturb_outer_cycles

(

"loops:perturb_outer_cycles"

)

BooleanOptionKey const loops::ramp_fa_rep

(

"loops:ramp_fa_rep"

)

BooleanOptionKey const loops::ramp_rama

(

"loops:ramp_rama"

)

RealOptionKey const loops::random_grow_loops_by

(

"loops:random_grow_loops_by"

)

BooleanOptionKey const loops::random_loop

(

"loops:random_loop"

)

BooleanOptionKey const loops::random_order

(

"loops:random_order"

)

StringOptionKey const loops::refine

(

"loops:refine"

)

IntegerOptionKey const loops::refine_design_iterations

(

"loops:refine_design_iterations"

)

RealOptionKey const loops::refine_final_temp

(

"loops:refine_final_temp"

)

RealOptionKey const loops::refine_init_temp

(

"loops:refine_init_temp"

)

BooleanOptionKey const loops::refine_only

(

"loops:refine_only"

)

IntegerOptionKey const loops::refine_outer_cycles

(

"loops:refine_outer_cycles"

)

StringOptionKey const loops::relax

(

"loops:relax"

)

BooleanOptionKey const loops::relax_with_foldtree

(

"loops:relax_with_foldtree"

)

StringOptionKey const loops::remodel

(

"loops:remodel"

)

RealOptionKey const loops::remodel_final_temp

(

"loops:remodel_final_temp"

)

RealOptionKey const loops::remodel_init_temp

(

"loops:remodel_init_temp"

)

IntegerOptionKey const loops::remodel_kic_attempts

(

"loops:remodel_kic_attempts"

)

BooleanOptionKey const loops::remove_extended_loops

(

"loops:remove_extended_loops"

)

IntegerOptionKey const loops::repack_period

(

"loops:repack_period"

)

StringOptionKey const loops::restrict_kic_sampling_to_torsion_string

(

"loops:restrict_kic_sampling_to_torsion_string"

)

RealOptionKey const loops::rmsd_tol

(

"loops:rmsd_tol"

)

BooleanOptionKey const loops::sample_omega_at_pre_prolines

(

"loops:sample_omega_at_pre_prolines"

)

RealOptionKey const loops::score_filter_cutoff

(

"loops:score_filter_cutoff"

)

RealOptionKey const loops::scored_frag_cycles

(

"loops:scored_frag_cycles"

)

IntegerOptionKey const loops::select_best_loop_from

(

"loops:select_best_loop_from"

)

RealOptionKey const loops::short_frag_cycles

(

"loops:short_frag_cycles"

)

BooleanOptionKey const loops::shorten_long_terminal_loop

(

"loops:shorten_long_terminal_loop"

)

RealOptionKey const loops::skip_1mers

(

"loops:skip_1mers"

)

RealOptionKey const loops::skip_3mers

(

"loops:skip_3mers"

)

RealOptionKey const loops::skip_9mers

(

"loops:skip_9mers"

)

BooleanOptionKey const loops::skip_ccd_moves

(

"loops:skip_ccd_moves"

)

BooleanOptionKey const loops::skip_initial_loop_build

(

"loops:skip_initial_loop_build"

)

IntegerOptionKey const loops::spread

(

"loops:spread"

)

FileVectorOptionKey const loops::stealfrags

(

"loops:stealfrags"

)

IntegerOptionKey const loops::stealfrags_times

(

"loops:stealfrags_times"

)

BooleanOptionKey const loops::strict_loops

(

"loops:strict_loops"

)

BooleanOptionKey const loops::superimpose_native

(

"loops:superimpose_native"

)

BooleanOptionKey const loops::taboo_in_fa

(

"loops:taboo_in_fa"

)

BooleanOptionKey const loops::taboo_sampling

(

"loops:taboo_sampling"

)

BooleanOptionKey const loops::timer

(

"loops:timer"

)

FileOptionKey const loops::vall_file

(

"loops:vall_file"

)

RealOptionKey const loops::vicinity_degree

(

"loops:vicinity_degree"

)

BooleanOptionKey const loops::vicinity_sampling

(

"loops:vicinity_sampling"

)

Variable Documentation

tuple loops.ccd_closure = CCDLoopClosureMover(my_loop, movemap)

Referenced by add_rosetta_options_4().

int loops.cutpoint = 81

float loops.final_temp = 0.8

tuple loops.fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")

tuple loops.gamma = math.pow((final_temp/init_temp),(1.0/(outer_cycles*inner_cycles)))

float loops.init_temp = 2.0

int loops.inner_cycles = 30

tuple loops.jd = Job_dist("loop_output", 100, scorefxn_high)

loops.kT = init_temp

int loops.loop_begin = 77

int loops.loop_end = 85

tuple loops.loop_refine = LoopMover_Refine_CCD(my_loops)

tuple loops.Lrms = loop_rmsd(p, starting_p, my_loops, True)

tuple loops.mc = MonteCarlo(p, scorefxn_low, kT)

tuple loops.movemap = MoveMap()

tuple loops.mover_3mer = ClassicFragmentMover(fragset3mer,movemap)

tuple loops.my_loop = Loop( loop_begin, loop_end, cutpoint)

tuple loops.my_loops = Loops()

int loops.outer_cycles = 10

tuple loops.p = Pose()

tuple loops.pack = protocols.simple_moves.PackRotamersMover( scorefxn_high, task_pack )

Referenced by CoupledMovesProtocol.apply(), main(), packmin_unbound_pep(), InteractionGraphPerformanceBenchmark.prepare_rotamer_sets(), rebuild_test(), repack_test(), InteractionGraphPerformanceBenchmark.run(), ConsensusFragmentMover.run(), and SolutionRescoreMover.run().

tuple loops.recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p)

tuple loops.scorefxn_high = create_score_function_ws_patch('standard', 'score12')

tuple loops.scorefxn_low = create_score_function('cen_std')

tuple loops.starting_p = Pose()

tuple loops.starting_p_centroid = Pose()

tuple loops.task_pack = TaskFactory.create_packer_task(starting_p)

tuple loops.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid')

tuple loops.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard')